Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015312.1 Kokia drynarioides strain JFW-HI SEQ_130357, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 167290
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 277 characters in sequence are not A, C, G, or T
Found at i:5914 original size:50 final size:50
Alignment explanation
Indices: 5834--5940 Score: 164
Period size: 50 Copynumber: 2.1 Consensus size: 50
5824 CATACAATCT
*
5834 TTTCTTATTTATCTAAATAGATAAAGGGAAAGTAAGAAACACATAATAAA
1 TTTCTTATTTATCTAAATAGATAAAAGGAAAGTAAGAAACACATAATAAA
*
5884 TTTCTATATTT-TCTAAATATATAAAAGGAAAGTAAGAAACACATAAT-AA
1 TTTCT-TATTTATCTAAATAGATAAAAGGAAAGTAAGAAACACATAATAAA
5933 TTTGCTTA
1 TTT-CTTA
5941 AAGTTTATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
49 7 0.13
50 41 0.77
51 5 0.09
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (50 bp):
TTTCTTATTTATCTAAATAGATAAAAGGAAAGTAAGAAACACATAATAAA
Found at i:6647 original size:9 final size:9
Alignment explanation
Indices: 6633--6665 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
6623 GTGTAATCAA
6633 CACCTTGAT
1 CACCTTGAT
*
6642 CACCTTCAT
1 CACCTTGAT
6651 CACCTTGAT
1 CACCTTGAT
6660 CACCTT
1 CACCTT
6666 CAACTGGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.21, C:0.39, G:0.06, T:0.33
Consensus pattern (9 bp):
CACCTTGAT
Found at i:6656 original size:18 final size:18
Alignment explanation
Indices: 6633--6667 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
6623 GTGTAATCAA
6633 CACCTTGATCACCTTCAT
1 CACCTTGATCACCTTCAT
6651 CACCTTGATCACCTTCA
1 CACCTTGATCACCTTCA
6668 ACTGGATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.06, T:0.31
Consensus pattern (18 bp):
CACCTTGATCACCTTCAT
Found at i:8285 original size:32 final size:32
Alignment explanation
Indices: 8220--8286 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
8210 TTAAAATCTA
*
8220 AAACTCGAAACATGATGTAAACCATAAACTTT
1 AAACTCGAAACATGATATAAACCATAAACTTT
** *
8252 AAACTCGAAATTTGATATAAAACCA-AAATTTT
1 AAACTCGAAACATGATAT-AAACCATAAACTTT
8284 AAA
1 AAA
8287 TCTTAAATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 24 0.80
33 6 0.20
ACGTcount: A:0.51, C:0.15, G:0.07, T:0.27
Consensus pattern (32 bp):
AAACTCGAAACATGATATAAACCATAAACTTT
Found at i:13454 original size:19 final size:18
Alignment explanation
Indices: 13429--13502 Score: 78
Period size: 19 Copynumber: 4.0 Consensus size: 18
13419 AGAGAATAGA
*
13429 AATACTGGCTCATAAGAG
1 AATACTGGCTCGTAAGAG
*
13447 AGATACTGGCTCGT-TGAG
1 A-ATACTGGCTCGTAAGAG
*
13465 CAATATTGGCTCGTAAGAG
1 -AATACTGGCTCGTAAGAG
*
13484 AAATACTAGCTCGTAAGAG
1 -AATACTGGCTCGTAAGAG
13503 CATTATTGGA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
18 15 0.33
19 31 0.67
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (18 bp):
AATACTGGCTCGTAAGAG
Found at i:13484 original size:37 final size:38
Alignment explanation
Indices: 13429--13511 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 38
13419 AGAGAATAGA
* * * *
13429 AATACTGGCTCATAAGAGAGATACTGGCTCGT-TGAGC
1 AATATTGGCTCATAAGAGAAATACTAGCTCGTAAGAGC
*
13466 AATATTGGCTCGTAAGAGAAATACTAGCTCGTAAGAGC
1 AATATTGGCTCATAAGAGAAATACTAGCTCGTAAGAGC
*
13504 ATTATTGG
1 AATATTGG
13512 ATCACAAGGA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
37 28 0.72
38 11 0.28
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.27
Consensus pattern (38 bp):
AATATTGGCTCATAAGAGAAATACTAGCTCGTAAGAGC
Found at i:24094 original size:30 final size:29
Alignment explanation
Indices: 24060--24275 Score: 98
Period size: 30 Copynumber: 7.3 Consensus size: 29
24050 TAATTTCGAA
24060 AAAGTTTAAGGGTAAAAATGTAATTTTGGG
1 AAAGTTT-AGGGTAAAAATGTAATTTTGGG
* *
24090 AAAGTTTAGGGTCAAAATGTGATTTT-GG
1 AAAGTTTAGGGTAAAAATGTAATTTTGGG
* * * * * *
24118 AGGAGTTTGGCGGTCAAAAT-AAATTTTTAGA
1 A-AAGTTTAG-GGTAAAAATGTAA-TTTTGGG
* * * *
24149 AAAGTTTGAGGGTCAAAATGTGATTTTAGA
1 AAAGTTT-AGGGTAAAAATGTAATTTTGGG
* * ** *
24179 AAAGTTTGGAGGTTAAAATCCAATTTTGGA
1 AAAGTTTAG-GGTAAAAATGTAATTTTGGG
* * * *
24209 AAAGTTAAGGGGTCAAAGTATAATTTT-GG
1 AAAGTTTA-GGGTAAAAATGTAATTTTGGG
* * **
24238 AGAAGTTTGGGAGTCAAAATGGGATTTTGGG
1 A-AAGTTTAGG-GTAAAAATGTAATTTTGGG
24269 -AAGTTTA
1 AAAGTTTA
24276 AGGACCTTTA
Statistics
Matches: 144, Mismatches: 31, Indels: 23
0.73 0.16 0.12
Matches are distributed among these distances:
28 3 0.02
29 35 0.24
30 99 0.69
31 7 0.05
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.33
Consensus pattern (29 bp):
AAAGTTTAGGGTAAAAATGTAATTTTGGG
Found at i:24173 original size:60 final size:58
Alignment explanation
Indices: 24081--24257 Score: 185
Period size: 60 Copynumber: 3.0 Consensus size: 58
24071 GTAAAAATGT
* * *
24081 AATTTTGGGAAAGTTTAGGGTCAAAATGTGATTTTGGAGGAGTTTGGCGGTCAAAAT-A
1 AATTTTAGAAAAGTTTAGGGTCAAAATGTGATTTTGGAGAAGTTTGG-GGTCAAAATCA
* * * *
24139 AATTTTTAGAAAAGTTTGAGGGTCAAAATGTGATTTTAGAAAAGTTTGGAGGTTAAAATCC
1 AA-TTTTAGAAAAGTTT-AGGGTCAAAATGTGATTTTGGAGAAGTTTGG-GGTCAAAATCA
* * * * *
24200 AATTTTGGAAAAGTTAAGGGGTCAAAGTATAATTTTGGAGAAGTTTGGGAGTCAAAAT
1 AATTTTAGAAAAGTTTA-GGGTCAAAATGTGATTTTGGAGAAGTTTGGG-GTCAAAAT
24258 GGGATTTTGG
Statistics
Matches: 98, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
58 2 0.02
59 14 0.14
60 80 0.82
61 2 0.02
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.33
Consensus pattern (58 bp):
AATTTTAGAAAAGTTTAGGGTCAAAATGTGATTTTGGAGAAGTTTGGGGTCAAAATCA
Found at i:25167 original size:30 final size:27
Alignment explanation
Indices: 25102--25158 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
25092 CTTTTTTTTT
25102 GCAGGTGATCACGTGGTGGTGGCAGAG
1 GCAGGTGATCACGTGGTGGTGGCAGAG
*
25129 GCAGGTGATCACGTGGTGGTGGTAGAG
1 GCAGGTGATCACGTGGTGGTGGCAGAG
25156 GCA
1 GCA
25159 AGTGGTGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.19, C:0.14, G:0.47, T:0.19
Consensus pattern (27 bp):
GCAGGTGATCACGTGGTGGTGGCAGAG
Found at i:26393 original size:49 final size:49
Alignment explanation
Indices: 26327--26788 Score: 401
Period size: 49 Copynumber: 9.3 Consensus size: 49
26317 TAAGGTGCTA
* *
26327 GGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCATGGTACTG
1 GGTTCACCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCG
* ** * * * *
26376 GGTTCACCATTACGGCCTCAACCTTTCCCATCACATCTTTTAAGGTACCG
1 GGTTCACCGTTGTGGCCTCAACCTTTCCCTTCATATC-TTCATGGTACCG
* ** * * * *
26426 GATTTGCCATCGTGGCCTCAATCC-TTCCCTTCATCTCTGCATGGTACCG
1 GGTTCACCGTTGTGGCCTCAA-CCTTTCCCTTCATATCTTCATGGTACCG
* * ** * *
26475 TGTT-AGCCGTTGTGGCCTCAACCTTT-CCTATCACATCTTTTTAAGTATCG
1 GGTTCA-CCGTTGTGGCCTCAACCTTTCCCT-TCATATCTTCAT-GGTACCG
* * *
26525 GGTTCACCGTTGCGGCCTCAATCTTTCCCTTCATATCTTCATGGTATCG
1 GGTTCACCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCG
* * * * * *
26574 GGTTCTCCGTTGCGACCTCAACCTTTCCCATCACATCTTCTAGGGTACCG
1 GGTTCACCGTTGTGGCCTCAACCTTTCCCTTCATATCTTC-ATGGTACCG
* * * * * *
26624 GATTCGCCGTTGTGGCCTCAATCC-TTCCTTTCATCTCTTCCTAGTACCG
1 GGTTCACCGTTGTGGCCTCAA-CCTTTCCCTTCATATCTTCATGGTACCG
** * * * *
26673 GGTTTGCCGTTGTGGCCACAACCTTTCCCATCACATCTTCTTAGGTACCG
1 GGTTCACCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCAT-GGTACCG
* * *
26723 AGTTCACCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCGTGGTATCG
1 GGTTCACCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCG
*
26772 GGTTCGCCGTTGTGGCC
1 GGTTCACCGTTGTGGCC
26789 ACATCTTCTA
Statistics
Matches: 324, Mismatches: 77, Indels: 24
0.76 0.18 0.06
Matches are distributed among these distances:
48 7 0.02
49 163 0.50
50 146 0.45
51 8 0.02
ACGTcount: A:0.15, C:0.32, G:0.19, T:0.34
Consensus pattern (49 bp):
GGTTCACCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCG
Found at i:26684 original size:198 final size:198
Alignment explanation
Indices: 26327--27034 Score: 664
Period size: 198 Copynumber: 3.7 Consensus size: 198
26317 TAAGGTGCTA
* * * *
26327 GGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCATGGTA-CTGGGTTCACCATTACGG
1 GGTTCACCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCATGGTATC-GGGTTCACCGTTGCGA
* *
26391 CCTCAACCTTTCCCATCACATCTTTTAAGGTACCGGATTTGCCATCGTGGCCTCAATCCTTCCCT
65 CCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGATTCGCCATCGTGGCCTCAATCCTTCCCT
* * * * *
26456 TCATCTCTGCATGGTACCGTGTTAGCCGTTGTGGCCTCAACCTTTCCTATCACATCTTTTTAAGT
130 TCATCTCTGCATAGTACCGGGTTAGCCGTTGTGGCCACAACCTTTCCCATCACATCTTCTTAAGT
*
26521 ATCG
195 ACCG
* * *
26525 GGTTCACCGTTGCGGCCTCAATCTTTCCCTTCATATCTTCATGGTATCGGGTTCTCCGTTGCGAC
1 GGTTCACCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCGGGTTCACCGTTGCGAC
* * * *
26590 CTCAACCTTTCCCATCACATCTTCTAGGGTACCGGATTCGCCGTTGTGGCCTCAATCCTTCCTTT
66 CTCAACCTTTCCCATCACATCTTCTAAGGTACCGGATTCGCCATCGTGGCCTCAATCCTTCCCTT
* * * *
26655 CATCTCTTCCTAGTACCGGGTTTGCCGTTGTGGCCACAACCTTTCCCATCACATCTTCTTAGGTA
131 CATCTCTGCATAGTACCGGGTTAGCCGTTGTGGCCACAACCTTTCCCATCACATCTTCTTAAGTA
26720 CCG
196 CCG
* * *
26723 AGTTCACCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCGTGGTATCGGGTTCGCCGTT--G--
1 GGTTCACCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCGGGTTCACCGTTGCGAC
** * ** * * *
26784 ---------TGGC--CACATCTTCTAAGGTACTGGATTCATCGTCGCGGCCTTAATCCTTCCCTT
66 CTCAACCTTTCCCATCACATCTTCTAAGGTACCGGATTCGCCATCGTGGCCTCAATCCTTCCCTT
* * * * * * * * * ** * * * *
26838 CATCTCTTCATGGTAGCGGGTTCGTCGTTATGGTCTCAACCCTTCCTTTTACATCTTCAT-GGCA
131 CATCTCTGCATAGTACCGGGTTAGCCGTTGTGGCCACAACCTTTCCCATCACATCTTCTTAAGTA
26902 CCG
196 CCG
** * * * *
26905 GGTTCACCGTTACGGCCTCAACCTTTCCCATCACATCTTCTTAGGTA-CTGGGTTC-CTCATTGC
1 GGTTCACCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCAT-GGTATC-GGGTTCAC-CGTTGC
* * * * * ***
26968 GGCATCAACCTTTCCCTTCACATCTTTTAAGGTACCGGATTTG-CAGTCACAGCCTCAATCCTTC
63 GACCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGATTCGCCA-TCGTGGCCTCAATCCTTC
27032 CCT
127 CCT
27035 GTCAAACCTA
Statistics
Matches: 421, Mismatches: 69, Indels: 40
0.79 0.13 0.08
Matches are distributed among these distances:
182 44 0.10
183 102 0.24
185 3 0.01
196 3 0.01
197 1 0.00
198 267 0.63
199 1 0.00
ACGTcount: A:0.16, C:0.32, G:0.18, T:0.34
Consensus pattern (198 bp):
GGTTCACCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCGGGTTCACCGTTGCGAC
CTCAACCTTTCCCATCACATCTTCTAAGGTACCGGATTCGCCATCGTGGCCTCAATCCTTCCCTT
CATCTCTGCATAGTACCGGGTTAGCCGTTGTGGCCACAACCTTTCCCATCACATCTTCTTAAGTA
CCG
Found at i:26791 original size:99 final size:98
Alignment explanation
Indices: 26327--26788 Score: 536
Period size: 99 Copynumber: 4.7 Consensus size: 98
26317 TAAGGTGCTA
* * * **
26327 GGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCATGGTACTGGGTTCACCATTACGGC
1 GGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTCGCCGTTGTGGC
26392 CTCAACCTTTCCCATCACATCTT-TTAAGGTACC
66 CTCAACCTTTCCCATCACATCTTCTT-AGGTACC
* * * * * * *
26425 GGATTTGCCATCGTGGCCTCAATCC-TTCCCTTCATCTCTGCATGGTACCGTGTTAGCCGTTGTG
1 GG-TTCGCCGTTGTGGCCTCAA-CCTTTCCCTTCATATCTTCATGGTACCGGGTTCGCCGTTGTG
* * * *
26489 GCCTCAACCTTTCCTATCACATCTTTTTAAGTATCG
64 GCCTCAACCTTTCCCATCACATCTTCTTAGGTA-CC
* * * * * * *
26525 GGTTCACCGTTGCGGCCTCAATCTTTCCCTTCATATCTTCATGGTATCGGGTTCTCCGTTGCGAC
1 GGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTCGCCGTTGTGGC
26590 CTCAACCTTTCCCATCACATCTTC-TAGGGTACC
66 CTCAACCTTTCCCATCACATCTTCTTA-GGTACC
* * * * *
26623 GGATTCGCCGTTGTGGCCTCAATCC-TTCCTTTCATCTCTTCCTAGTACCGGGTTTGCCGTTGTG
1 GG-TTCGCCGTTGTGGCCTCAA-CCTTTCCCTTCATATCTTCATGGTACCGGGTTCGCCGTTGTG
*
26687 GCCACAACCTTTCCCATCACATCTTCTTAGGTACC
64 GCCTCAACCTTTCCCATCACATCTTCTTAGGTACC
* * *
26722 GAGTTCACCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCGTGGTATCGGGTTCGCCGTTGTGG
1 G-GTTCGCCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTCGCCGTTGTGG
26787 CC
65 CC
26789 ACATCTTCTA
Statistics
Matches: 300, Mismatches: 53, Indels: 21
0.80 0.14 0.06
Matches are distributed among these distances:
98 10 0.03
99 279 0.93
100 11 0.04
ACGTcount: A:0.15, C:0.32, G:0.19, T:0.34
Consensus pattern (98 bp):
GGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTCGCCGTTGTGGC
CTCAACCTTTCCCATCACATCTTCTTAGGTACC
Found at i:26846 original size:84 final size:84
Alignment explanation
Indices: 26704--26866 Score: 204
Period size: 84 Copynumber: 1.9 Consensus size: 84
26694 CCTTTCCCAT
* * * *
26704 CACATCTTCTTAGGTACCGAGTTCACCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCGTGGTA
1 CACATCTTCTAAGGTACCGAGTTCACCGTCGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTA
*
26769 TCGGGTTCGCCGTTGTGGC
66 GCGGGTTCGCCGTTGTGGC
* * * *
26788 CACATCTTCTAAGGTACTG-GATTCATCGTCGCGGCCTTAATCC-TTCCCTTCATCTCTTCATGG
1 CACATCTTCTAAGGTACCGAG-TTCACCGTCGCGGCCTCAA-CCTTTCCCTTCATATCTTCATGG
*
26851 TAGCGGGTTCGTCGTT
64 TAGCGGGTTCGCCGTT
26867 ATGGTCTCAA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
83 1 0.01
84 64 0.96
85 2 0.03
ACGTcount: A:0.14, C:0.29, G:0.21, T:0.35
Consensus pattern (84 bp):
CACATCTTCTAAGGTACCGAGTTCACCGTCGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTA
GCGGGTTCGCCGTTGTGGC
Found at i:26883 original size:49 final size:49
Alignment explanation
Indices: 26819--26993 Score: 138
Period size: 49 Copynumber: 3.6 Consensus size: 49
26809 TTCATCGTCG
* * * * **
26819 CGGCCTTAATCCTTCCCTTCATC-TCTTCATGGTAGCGGGTTCGTCGTTA
1 CGGCCTCAACCCTTCCCTTCA-CATCTTCATGGCACCGGGTTCACCGTTA
* * * *
26868 TGGTCTCAACCCTTCCTTTTACATCTTCATGGCACCGGGTTCACCGTTA
1 CGGCCTCAACCCTTCCCTTCACATCTTCATGGCACCGGGTTCACCGTTA
* * * * * * *
26917 CGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACTGGGTTC-CTCATTG
1 CGGCCTCAACCCTTCCCTTCACATCTTCAT-GGCACCGGGTTCAC-CGTTA
* *
26967 CGGCATCAACCTTTCCCTTCACATCTT
1 CGGCCTCAACCCTTCCCTTCACATCTT
26994 TTAAGGTACC
Statistics
Matches: 100, Mismatches: 23, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
48 1 0.01
49 61 0.61
50 38 0.38
ACGTcount: A:0.15, C:0.34, G:0.16, T:0.35
Consensus pattern (49 bp):
CGGCCTCAACCCTTCCCTTCACATCTTCATGGCACCGGGTTCACCGTTA
Found at i:27984 original size:8 final size:8
Alignment explanation
Indices: 27982--28054 Score: 60
Period size: 8 Copynumber: 8.9 Consensus size: 8
27972 ATTTTTCCCT
27982 TTTTTCTTC
1 TTTTTC-TC
*
27991 TTTTTTTC
1 TTTTTCTC
27999 TTTTT-TCC
1 TTTTTCT-C
28007 ATTTTTCTC
1 -TTTTTCTC
28016 TTTTTCTC
1 TTTTTCTC
* *
28024 TTTTTTTA
1 TTTTTCTC
28032 TTTTTCTTC
1 TTTTTC-TC
*
28041 TTCTTCT-
1 TTTTTCTC
28048 TTTTTCT
1 TTTTTCT
28055 TTCTTTTTTC
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
7 7 0.13
8 28 0.53
9 17 0.32
10 1 0.02
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTCTC
Found at i:27989 original size:33 final size:33
Alignment explanation
Indices: 27949--28068 Score: 106
Period size: 33 Copynumber: 3.6 Consensus size: 33
27939 TCTCCTTTTC
27949 TTTTTCTTTTCTTTTTCTATTTT-ATTTTTCCCT
1 TTTTTCTTTT-TTTTTCTATTTTCATTTTTCCCT
* *
27982 TTTTTCTTCTTTTTTTCTTTTTTCCATTTTTCTC-
1 TTTTTCTT-TTTTTTTCTATTTT-CATTTTTCCCT
* * * *
28016 TTTTTCTCTTTTTTTAT-TTTTC-TTCTTCTTCT
1 TTTTTCTTTTTTTTTCTATTTTCATTTTTC-CCT
28048 TTTTTCTTTCTTTTTTC-ATTT
1 TTTTTCTTT-TTTTTTCTATTT
28069 ATTTCATTGA
Statistics
Matches: 73, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
30 5 0.07
31 3 0.04
32 12 0.16
33 36 0.49
34 9 0.12
35 8 0.11
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (33 bp):
TTTTTCTTTTTTTTTCTATTTTCATTTTTCCCT
Found at i:28017 original size:25 final size:25
Alignment explanation
Indices: 27968--28053 Score: 86
Period size: 26 Copynumber: 3.5 Consensus size: 25
27958 TCTTTTTCTA
* * *
27968 TTTTATTTTTCCCTTTTTTCTTCTTT
1 TTTTCTTTTTTCCATTTTTC-TCTTT
27994 TTTTCTTTTTTCCATTTTTCTCTTT
1 TTTTCTTTTTTCCATTTTTCTCTTT
* * *
28019 TTCTCTTTTTT-TATTTTTCT-TCT
1 TTTTCTTTTTTCCATTTTTCTCTTT
*
28042 TCTTCTTTTTTC
1 TTTTCTTTTTTC
28054 TTTCTTTTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
23 11 0.22
24 8 0.16
25 15 0.29
26 17 0.33
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTCTTTTTTCCATTTTTCTCTTT
Found at i:28027 original size:16 final size:16
Alignment explanation
Indices: 27982--28054 Score: 60
Period size: 17 Copynumber: 4.4 Consensus size: 16
27972 ATTTTTCCCT
*
27982 TTTTTCTTCTTTTTTTC
1 TTTTTC-TCTTTTTCTC
27999 TTTTT-TCCATTTTTCTC
1 TTTTTCT-C-TTTTTCTC
* *
28016 TTTTTCTCTTTTTTTA
1 TTTTTCTCTTTTTCTC
*
28032 TTTTTCTTCTTCTTCT-
1 TTTTTC-TCTTTTTCTC
28048 TTTTTCT
1 TTTTTCT
28055 TTCTTTTTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
15 2 0.04
16 19 0.40
17 25 0.53
18 1 0.02
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTCTCTTTTTCTC
Found at i:28061 original size:25 final size:23
Alignment explanation
Indices: 27983--28063 Score: 55
Period size: 25 Copynumber: 3.5 Consensus size: 23
27973 TTTTTCCCTT
*
27983 TTTTCTTCTTTTTTTCTTTTTTCC
1 TTTTCTTC-TTTTTTCTTTTTTTC
*
28007 ATTTT-TCTCTTTTTCTCTTTTTTTAT
1 -TTTTCT-TCTTTTT-TCTTTTTTT-C
*
28033 TTTTCTTC-TTCTTC-TTTTTTC
1 TTTTCTTCTTTTTTCTTTTTTTC
28054 -TTTCTT-TTTT
1 TTTTCTTCTTTT
28064 CATTTATTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 15
0.70 0.08 0.23
Matches are distributed among these distances:
20 8 0.17
22 6 0.13
23 2 0.04
24 9 0.20
25 20 0.43
26 1 0.02
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTCTTCTTTTTTCTTTTTTTC
Found at i:33059 original size:30 final size:30
Alignment explanation
Indices: 32873--33089 Score: 143
Period size: 30 Copynumber: 7.2 Consensus size: 30
32863 AATTTCGTAA
* * *
32873 AAGTTTAAGGGTAAAAATGTAATTTTTGG-G
1 AAGTTTAGGGGTCAAAATG-AAATTTTGGAG
**
32903 AAAGTTT-GGGGTCAAAAATGTGATTTTGGAG
1 -AAGTTTAGGGGTC-AAAATGAAATTTTGGAG
* * * *
32934 GAGTTTGGGGGTCAAAATAAAATTTTGGAA
1 AAGTTTAGGGGTCAAAATGAAATTTTGGAG
* ** ** ** * *
32964 AAGTTCAAAGGTTTAAATGTGATTTTAGAA
1 AAGTTTAGGGGTCAAAATGAAATTTTGGAG
* * *
32994 AAGGTTAGAGGTCAAAATGAAATTTTGGAA
1 AAGTTTAGGGGTCAAAATGAAATTTTGGAG
** * *
33024 AAGTTTAGGTTTCAAAGTGTAATTTTGGAG
1 AAGTTTAGGGGTCAAAATGAAATTTTGGAG
**
33054 AAGTTTAGGGGTCAAAATGGGATTTTGG-G
1 AAGTTTAGGGGTCAAAATGAAATTTTGGAG
33083 AAGTTTA
1 AAGTTTA
33090 AGGACCTTCA
Statistics
Matches: 142, Mismatches: 41, Indels: 8
0.74 0.21 0.04
Matches are distributed among these distances:
29 8 0.06
30 115 0.81
31 19 0.13
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (30 bp):
AAGTTTAGGGGTCAAAATGAAATTTTGGAG
Found at i:33072 original size:60 final size:59
Alignment explanation
Indices: 32873--33089 Score: 197
Period size: 60 Copynumber: 3.6 Consensus size: 59
32863 AATTTCGTAA
* * * * **
32873 AAGTTTAAGGGTAAAAATGTAATTTTTGGGAAAGTTT-GGGGTCAAAAATGTGATTTTGGAG
1 AAGTTTAGGGGTCAAAATG-AAATTTTGGAAAAGTTTAGGTTTC--AAATGTGATTTTGGAG
* * * * * *
32934 GAGTTTGGGGGTCAAAATAAAATTTTGGAAAAGTTCAAAGGTTT-AAATGTGATTTTAGAA
1 AAGTTTAGGGGTCAAAATGAAATTTTGGAAAAGTT--TAGGTTTCAAATGTGATTTTGGAG
* * *
32994 AAGGTTAGAGGTCAAAATGAAATTTTGGAAAAGTTTAGGTTTCAAAGTGTAATTTTGGAG
1 AAGTTTAGGGGTCAAAATGAAATTTTGGAAAAGTTTAGGTTTCAAA-TGTGATTTTGGAG
** *
33054 AAGTTTAGGGGTCAAAATGGGATTTTGG-GAAGTTTA
1 AAGTTTAGGGGTCAAAATGAAATTTTGGAAAAGTTTA
33090 AGGACCTTCA
Statistics
Matches: 125, Mismatches: 26, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
58 6 0.05
59 10 0.08
60 92 0.74
61 14 0.11
63 3 0.02
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (59 bp):
AAGTTTAGGGGTCAAAATGAAATTTTGGAAAAGTTTAGGTTTCAAATGTGATTTTGGAG
Found at i:39197 original size:30 final size:31
Alignment explanation
Indices: 39145--39217 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
39135 CAACCCGCTC
* *
39145 ATATTATTT-TTTTAATTTTTTAA-AATATTT
1 ATATTTTTTATTTTAATTATTTAATAAT-TTT
39175 ATATTTTTTATTTTAA-TATTTAATAATTTT
1 ATATTTTTTATTTTAATTATTTAATAATTTT
*
39205 TTATTTTTTATTT
1 ATATTTTTTATTT
39218 ATTGAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 29 0.76
31 9 0.24
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (31 bp):
ATATTTTTTATTTTAATTATTTAATAATTTT
Found at i:39203 original size:23 final size:21
Alignment explanation
Indices: 39168--39219 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 21
39158 AATTTTTTAA
39168 AATATTTATATTTTTTATTTT
1 AATATTTATATTTTTTATTTT
39189 AATATTTAATAATTTTTTATTTT
1 AATATTT-AT-ATTTTTTATTTT
*
39212 -TTATTTAT
1 AATATTTAT
39220 TGAAAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 9 0.32
22 7 0.25
23 12 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
AATATTTATATTTTTTATTTT
Found at i:39218 original size:22 final size:22
Alignment explanation
Indices: 39168--39211 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
39158 AATTTTTTAA
39168 AATATTT-ATATTTTTTATTTT
1 AATATTTAATATTTTTTATTTT
39189 AATATTTAATAATTTTTTATTTT
1 AATATTTAAT-ATTTTTTATTTT
39212 TTATTTATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.33
22 2 0.10
23 12 0.57
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
AATATTTAATATTTTTTATTTT
Found at i:43414 original size:16 final size:17
Alignment explanation
Indices: 43384--43416 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
43374 TTTATAATAA
43384 CTTTAAAAACTCAAACC
1 CTTTAAAAACTCAAACC
43401 CTTTAAAAAC-CAAACC
1 CTTTAAAAACTCAAACC
43417 TAAGTCAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.21
Consensus pattern (17 bp):
CTTTAAAAACTCAAACC
Found at i:43546 original size:14 final size:15
Alignment explanation
Indices: 43522--43602 Score: 68
Period size: 13 Copynumber: 5.9 Consensus size: 15
43512 CTGTTGATCA
*
43522 TTGACCATTGACTCG
1 TTGACCGTTGACTCG
*
43537 TTGA-TGTTGA-TCG
1 TTGACCGTTGACTCG
43550 TTGACCGTTGACT-G
1 TTGACCGTTGACTCG
* *
43564 TTGA-CATTGAC-CA
1 TTGACCGTTGACTCG
43577 TTGACCGTTGACT--
1 TTGACCGTTGACTCG
*
43590 TTGACCATTGACT
1 TTGACCGTTGACT
43603 TTTTTCGAGA
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
13 29 0.54
14 20 0.37
15 5 0.09
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (15 bp):
TTGACCGTTGACTCG
Found at i:43560 original size:20 final size:20
Alignment explanation
Indices: 43522--43602 Score: 83
Period size: 20 Copynumber: 4.0 Consensus size: 20
43512 CTGTTGATCA
43522 TTGACCATTGACTCGTTGA-TG
1 TTGA-CATTGAC-CGTTGACTG
*
43543 TTGATCGTTGACCGTTGACTG
1 TTGA-CATTGACCGTTGACTG
* *
43564 TTGACATTGACCATTGACCG
1 TTGACATTGACCGTTGACTG
* *
43584 TTGACTTTGACCATTGACT
1 TTGACATTGACCGTTGACT
43603 TTTTTCGAGA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
20 36 0.69
21 16 0.31
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGACATTGACCGTTGACTG
Found at i:43561 original size:7 final size:7
Alignment explanation
Indices: 43522--43601 Score: 58
Period size: 7 Copynumber: 11.7 Consensus size: 7
43512 CTGTTGATCA
*
43522 TTGACCA
1 TTGACCG
43529 TTGACTCG
1 TTGAC-CG
*
43537 TTGA-TG
1 TTGACCG
*
43543 TTGATCG
1 TTGACCG
43550 TTGACCG
1 TTGACCG
*
43557 TTGACTG
1 TTGACCG
*
43564 TTGA-CA
1 TTGACCG
*
43570 TTGACCA
1 TTGACCG
43577 TTGACCG
1 TTGACCG
*
43584 TTGA-CT
1 TTGACCG
*
43590 TTGACCA
1 TTGACCG
43597 TTGAC
1 TTGAC
43602 TTTTTTCGAG
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
6 14 0.24
7 40 0.68
8 5 0.08
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (7 bp):
TTGACCG
Found at i:43580 original size:27 final size:27
Alignment explanation
Indices: 43515--43601 Score: 95
Period size: 27 Copynumber: 3.2 Consensus size: 27
43505 GACCAAACTG
* * **
43515 TTGATCATTGACCATTGACTCGTTGATG
1 TTGACCATTGACCGTTGACT-GTTGACA
* *
43543 TTGATCGTTGACCGTTGACTGTTGACA
1 TTGACCATTGACCGTTGACTGTTGACA
43570 TTGACCATTGACCGTTGACT-TTGACCA
1 TTGACCATTGACCGTTGACTGTTGA-CA
43597 TTGAC
1 TTGAC
43602 TTTTTTCGAG
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
26 4 0.08
27 30 0.58
28 18 0.35
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (27 bp):
TTGACCATTGACCGTTGACTGTTGACA
Found at i:44752 original size:22 final size:21
Alignment explanation
Indices: 44710--44755 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
44700 AAGTACATCC
44710 TATTTTGGGGATTTTAATATTT
1 TATTTTGGGGA-TTTAATATTT
44732 TATTTTGGGTGA-TTAATTATTT
1 TATTTTGGG-GATTTAA-TATTT
44754 TA
1 TA
44756 CTTAACTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.18
22 16 0.73
23 2 0.09
ACGTcount: A:0.24, C:0.00, G:0.17, T:0.59
Consensus pattern (21 bp):
TATTTTGGGGATTTAATATTT
Found at i:48079 original size:30 final size:29
Alignment explanation
Indices: 48032--48110 Score: 95
Period size: 30 Copynumber: 2.7 Consensus size: 29
48022 TTAGAGGTTC
*
48032 GAGGGTAAAACGGTAATTTTCGAACACTT
1 GAGGGTAAAATGGTAATTTTCGAACACTT
* * ***
48061 GAGGGTGAAAATGGTAATTTTTGGATGTTT
1 GAGGGT-AAAATGGTAATTTTCGAACACTT
48091 GAGGGTAAAATGGTAATTTT
1 GAGGGTAAAATGGTAATTTT
48111 GGACATTTCG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 20 0.47
30 23 0.53
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (29 bp):
GAGGGTAAAATGGTAATTTTCGAACACTT
Found at i:48128 original size:28 final size:29
Alignment explanation
Indices: 47987--48338 Score: 158
Period size: 29 Copynumber: 12.2 Consensus size: 29
47977 GTCAAAAATA
* * *
47987 TAATTTTT-GAATGCTCGGGGGTAAAATGG
1 TAATTTTTGGAAT-TTCGAGGGCAAAATGG
* ** * *
48016 TAATTTTTAGAGGTTCGAGGGTAAAACGG
1 TAATTTTTGGAATTTCGAGGGCAAAATGG
* * * *
48045 TAATTTTCGAACACTT-GAGGGTGAAAATGG
1 TAATTTTTGGA-ATTTCGAGGG-CAAAATGG
* *
48075 TAATTTTTGG-ATGTTTGAGGGTAAAATGG
1 TAATTTTTGGAAT-TTCGAGGGCAAAATGG
48104 TAA-TTTTGGACATTTCG-GGGCAAAATGG
1 TAATTTTTGGA-ATTTCGAGGGCAAAATGG
* *
48132 T-ATTTTTGGACA-CTCGAGGACAAAAT-G
1 TAATTTTTGGA-ATTTCGAGGGCAAAATGG
* *
48159 CAATTTTTGGAAGTTT-G-GGGTAAAATGG
1 TAATTTTTGGAA-TTTCGAGGGCAAAATGG
* * *
48187 TAATTTTTGGAAGTTCGAGAGCAAAACGG
1 TAATTTTTGGAATTTCGAGGGCAAAATGG
*** * *** *
48216 TAATTTTCAAAAAATTTGGAGTAAAAAATGA
1 TAATTTT--TGGAATTTCGAGGGCAAAATGG
* * **
48247 T-ATTTTTGGAAGTTCGAGGGTAAAATTA
1 TAATTTTTGGAATTTCGAGGGCAAAATGG
* *
48275 TAATTTTTGGAAGTTT-GGGGGAAAAAT-G
1 TAATTTTTGGAA-TTTCGAGGGCAAAATGG
* *
48303 TGATTTTTTGGAAGTTT-G-GAGCAAAATGG
1 T-AATTTTTGGAA-TTTCGAGGGCAAAATGG
48332 TAATTTT
1 TAATTTT
48339 GGATGCTCGG
Statistics
Matches: 246, Mismatches: 56, Indels: 43
0.71 0.16 0.12
Matches are distributed among these distances:
27 15 0.06
28 85 0.35
29 101 0.41
30 32 0.13
31 13 0.05
ACGTcount: A:0.32, C:0.06, G:0.27, T:0.35
Consensus pattern (29 bp):
TAATTTTTGGAATTTCGAGGGCAAAATGG
Found at i:48374 original size:85 final size:86
Alignment explanation
Indices: 48240--48396 Score: 194
Period size: 85 Copynumber: 1.8 Consensus size: 86
48230 TTTGGAGTAA
* * * * *
48240 AAAATGATATTTTTGGAAGTTCGAGGGTAAAATTATAATTTTTGGAAGTTTGGGGG-AAAAATGT
1 AAAATGATAATTTTGGAAGCTCGAGGGTAAAATTATAATTTTTGAAAGTTCGGGGGTAAAAATAT
*
48304 GATTTTTTGGAAGTTTGGAGC
66 AATTTTTTGGAAGTTTGGAGC
* * *
48325 AAAATGGTAATTTTGGATGCTCG-GGTGTAAAA-TGTAATTTTTAGAAAGTTCGGGGGTAAAAAT
1 AAAATGATAATTTTGGAAGCTCGAGG-GTAAAATTATAATTTTT-GAAAGTTCGGGGGTAAAAAT
48388 ATAATTTTT
64 ATAATTTTT
48397 GTAAAGTTCG
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
84 11 0.18
85 36 0.60
86 13 0.22
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (86 bp):
AAAATGATAATTTTGGAAGCTCGAGGGTAAAATTATAATTTTTGAAAGTTCGGGGGTAAAAATAT
AATTTTTTGGAAGTTTGGAGC
Found at i:48444 original size:57 final size:56
Alignment explanation
Indices: 47981--48606 Score: 233
Period size: 59 Copynumber: 10.8 Consensus size: 56
47971 AACGGAGTCA
* * * *
47981 AAAATATAATTTTT-GAATGCTCGGGGGTAAAATGGTAATTTTTAGAGGTTCGAGGGT-
1 AAAATATAATTTTTGGAA-GTTC-GGGGAAAAAT-GTAATTTTTGGAAGTTCGAGGGTC
** * * * * * *
48038 AAAACGGTAATTTTCGAACACTT-GAGGGTGAAAATGGTAATTTTTGGATGTTTGAGGGT-
1 AAAA-TATAATTTTTGGA-AGTTCG-GGG-AAAAAT-GTAATTTTTGGAAGTTCGAGGGTC
* * * * *
48097 AAAATGGTAA-TTTTGGACATTTCGGGGCAAAATGGT-ATTTTTGGACA-CTCGA-GGAC
1 AAAAT-ATAATTTTTGGA-AGTTCGGGGAAAAAT-GTAATTTTTGGA-AGTTCGAGGGTC
** * * *
48153 AAAATGCAATTTTTGGAAGTTTGGGGTAAAATGGTAATTTTTGGAAGTTCGAGAG-C
1 AAAATATAATTTTTGGAAGTTCGGGGAAAAAT-GTAATTTTTGGAAGTTCGAGGGTC
** *** * * *
48209 AAAACGGTAATTTTCAAAAAATTTGGAGTAAAAAATG-ATATTTTTGGAAGTTCGAGGGT-
1 AAAA-TATAATTTT-TGGAAGTTCGG-G-GAAAAATGTA-ATTTTTGGAAGTTCGAGGGTC
* * * *
48268 AAAATTATAATTTTTGGAAGTTTGGGGGAAAAATGTGATTTTTTGGAAGTTTG-GAG-C
1 AAAA-TATAATTTTTGGAAG-TTCGGGGAAAAATGT-AATTTTTGGAAGTTCGAGGGTC
* * * * * * *
48325 AAAATGGTAA-TTTTGGATGCTCGGGTGTAAAATGTAATTTTTAGAAAGTTCGGGGGTA
1 AAAAT-ATAATTTTTGGAAGTTCGGG-GAAAAATGTAATTTTT-GGAAGTTCGAGGGTC
*
48383 AAAATATAATTTTTGTAAAGTTCGAGGGAAAAATGT-A-TTTTGTGAAGTTCGAGGGTC
1 AAAATATAATTTTTG-GAAGTTCG-GGGAAAAATGTAATTTTTG-GAAGTTCGAGGGTC
* * * * * * * * *
48440 AAAATGTGA-TTTTGAAAAAGTTTGGGGTTAAAATATAATTTTTGGAAAATTTGATGGTC
1 AAAATATAATTTTTG--GAAGTTCGGGG-AAAAATGTAATTTTTGG-AAGTTCGAGGGTC
** * * ** *
48499 AAAATATAATTTTTTGGAAAGTTTACGGGTCAAAATGTGATTTTTGGAAATTTTTAGGGTT
1 AAAATATAA-TTTTTGG-AAG-TT-CGGGGAAAAATGTAATTTTTGG-AAGTTCGAGGGTC
* ** *
48560 AAAATATAATTTTTGGAAAGTTTAGGGGTCAAATGTGATTTTTGGAA
1 AAAATATAATTTTTGG-AAG-TTCGGGGAAAAATGTAATTTTTGGAA
48607 AATTCAGGGA
Statistics
Matches: 438, Mismatches: 89, Indels: 83
0.72 0.15 0.14
Matches are distributed among these distances:
55 31 0.07
56 75 0.17
57 77 0.18
58 61 0.14
59 126 0.29
60 25 0.06
61 40 0.09
62 3 0.01
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.36
Consensus pattern (56 bp):
AAAATATAATTTTTGGAAGTTCGGGGAAAAATGTAATTTTTGGAAGTTCGAGGGTC
Found at i:48453 original size:29 final size:29
Alignment explanation
Indices: 48239--48453 Score: 128
Period size: 29 Copynumber: 7.5 Consensus size: 29
48229 ATTTGGAGTA
*
48239 AAAAATGATATTTTTG-GAAGTTCGAGGGT
1 AAAAATG-TAATTTTGTGAAGTTCGAGGGT
* * * *
48268 AAAATTATAATTTT-TGGAAGTTTG-GGGG
1 AAAAATGTAATTTTGT-GAAGTTCGAGGGT
* * * *
48296 AAAAATGTGATTTTTTGGAAGTTTG-GAG-
1 AAAAATGTAATTTTGT-GAAGTTCGAGGGT
* * *
48324 CAAAATGGTAATTTTG-GATGCTCG-GGTGT
1 AAAAAT-GTAATTTTGTGAAGTTCGAGG-GT
*
48353 -AAAATGTAATTTT-TAGAAAGTTCGGGGGT
1 AAAAATGTAATTTTGT-G-AAGTTCGAGGGT
* *
48382 AAAAATATAATTTTTGTAAAGTTCGAGGG-
1 AAAAATGTAA-TTTTGTGAAGTTCGAGGGT
48411 AAAAATGT-ATTTTGTGAAGTTCGAGGGT
1 AAAAATGTAATTTTGTGAAGTTCGAGGGT
* *
48439 CAAAATGTGATTTTG
1 AAAAATGTAATTTTG
48454 AAAAAGTTTG
Statistics
Matches: 147, Mismatches: 24, Indels: 30
0.73 0.12 0.15
Matches are distributed among these distances:
27 31 0.21
28 40 0.27
29 51 0.35
30 20 0.14
31 4 0.03
32 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (29 bp):
AAAAATGTAATTTTGTGAAGTTCGAGGGT
Found at i:48574 original size:60 final size:60
Alignment explanation
Indices: 48477--48610 Score: 207
Period size: 61 Copynumber: 2.2 Consensus size: 60
48467 TTAAAATATA
*
48477 ATTTTTGGAAAATTTGATGGTCAAAATATAATTTTTTGGAAAGTTTACGGGTCAAAATGTG
1 ATTTTTGGAAAATTTGAGGGTCAAAATATAATTTTTTGGAAAGTTTACGGGTC-AAATGTG
* * * *
48538 ATTTTTGGAAATTTTTAGGGTTAAAATATAA-TTTTTGGAAAGTTTAGGGGTCAAATGTG
1 ATTTTTGGAAAATTTGAGGGTCAAAATATAATTTTTTGGAAAGTTTACGGGTCAAATGTG
48597 ATTTTTGGAAAATT
1 ATTTTTGGAAAATT
48611 CAGGGACCTT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 20 0.30
60 20 0.30
61 27 0.40
ACGTcount: A:0.34, C:0.03, G:0.22, T:0.42
Consensus pattern (60 bp):
ATTTTTGGAAAATTTGAGGGTCAAAATATAATTTTTTGGAAAGTTTACGGGTCAAATGTG
Found at i:48602 original size:29 final size:30
Alignment explanation
Indices: 48353--48607 Score: 163
Period size: 30 Copynumber: 8.6 Consensus size: 30
48343 GCTCGGGTGT
* * ** *
48353 AAAATGTAATTTTTAGAAAGTTCGGGGGTA
1 AAAATATAATTTTTGGAAAGTTTAGGGGTC
* * *
48383 AAAATATAATTTTTGTAAAG-TTCGAGGG-A
1 AAAATATAATTTTTGGAAAGTTTAG-GGGTC
* *
48412 AAAATGT-A-TTTTGTG-AAG-TTCGAGGGTC
1 AAAATATAATTTTTG-GAAAGTTTAG-GGGTC
* * * *
48440 AAAATGTGA-TTTTGAAAAAGTTT-GGGGTT
1 AAAATATAATTTTTG-GAAAGTTTAGGGGTC
* *
48469 AAAATATAATTTTTGGAAAATTT-GATGGTC
1 AAAATATAATTTTTGGAAAGTTTAG-GGGTC
*
48499 AAAATATAATTTTTTGGAAAGTTTACGGGTC
1 AAAATATAA-TTTTTGGAAAGTTTAGGGGTC
* * * *
48530 AAAATGTGATTTTTGGAAATTTTTA-GGGTT
1 AAAATATAATTTTTGGAAA-GTTTAGGGGTC
48560 AAAATATAATTTTTGGAAAGTTTAGGGGTC
1 AAAATATAATTTTTGGAAAGTTTAGGGGTC
* *
48590 -AAATGTGATTTTTGGAAA
1 AAAATATAATTTTTGGAAA
48608 ATTCAGGGAC
Statistics
Matches: 183, Mismatches: 30, Indels: 25
0.77 0.13 0.11
Matches are distributed among these distances:
27 16 0.09
28 8 0.04
29 53 0.29
30 76 0.42
31 30 0.16
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (30 bp):
AAAATATAATTTTTGGAAAGTTTAGGGGTC
Found at i:61350 original size:28 final size:27
Alignment explanation
Indices: 61319--61415 Score: 74
Period size: 28 Copynumber: 3.5 Consensus size: 27
61309 GTTCGGCGGT
61319 AAAATGATAATTTTGGAAACTTTGGGG
1 AAAATGATAATTTTGGAAACTTTGGGG
* * *
61346 CAAAATGGTAA-TTTGGACAC-TCGGGCG
1 -AAAATGATAATTTTGGAAACTTTGGG-G
* *
61373 TAAAAATG-TAATTTTTGAAAGTTTAGGGG
1 --AAAATGATAATTTTGGAAACTTT-GGGG
*
61402 TAAATGATAATTTT
1 AAAATGATAATTTT
61416 TAGAAGTTCG
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
26 4 0.07
27 17 0.31
28 28 0.52
29 2 0.04
30 3 0.06
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.34
Consensus pattern (27 bp):
AAAATGATAATTTTGGAAACTTTGGGG
Found at i:61775 original size:30 final size:30
Alignment explanation
Indices: 61462--61837 Score: 240
Period size: 30 Copynumber: 12.6 Consensus size: 30
61452 TTCGAAGTCA
* *
61462 AAAATG-ATATTTTTCG-AAGTTCGAGGG-T
1 AAAATGTA-ATTTTTGGAAAGTTTGAGGGTT
* **
61490 AAAATGGTAATTTTTGG-AAGTTCGAGGGCA
1 AAAAT-GTAATTTTTGGAAAGTTTGAGGGTT
* *
61520 AAAATGTGATTTTTTTTGG-AAGTTCG-GGG-T
1 AAAATGT-A--ATTTTTGGAAAGTTTGAGGGTT
*
61550 GAAATGGTAATTTTT-GAAAGTTTGAGGG-T
1 AAAAT-GTAATTTTTGGAAAGTTTGAGGGTT
* * *
61579 AAAATTTTAATTTTTGGAAAGTTCGAGGGTA
1 AAAA-TGTAATTTTTGGAAAGTTTGAGGGTT
* *
61610 AAAATGTAATTTTTGTG-AAGTTTAAGGGTA
1 AAAATGTAATTTTTG-GAAAGTTTGAGGGTT
*
61640 AAAATGTAATTTTTGTG-AAGTTCGAGGGTT
1 AAAATGTAATTTTTG-GAAAGTTTGAGGGTT
* * * *
61670 AAAATGTGATTTTAGAAAAGTTTTG-GAGTT
1 AAAATGTAATTTTTGGAAAG-TTTGAGGGTT
* * * * *
61700 AAAATATGATTTTTGGAAAATTTGACGGTC
1 AAAATGTAATTTTTGGAAAGTTTGAGGGTT
**
61730 AAAATACAATTTTTGGAAAGTTTGAGGGTT
1 AAAATGTAATTTTTGGAAAGTTTGAGGGTT
* * *
61760 AAAACGTAATTTTTGGAAAATTT-AGAGGTC
1 AAAATGTAATTTTTGGAAAGTTTGAG-GGTT
* * * *
61790 AAAATATAATTTTT-AAAAGTTTAAGGGTC
1 AAAATGTAATTTTTGGAAAGTTTGAGGGTT
* * *
61819 AAAACGTGATTTTTAGAAA
1 AAAATGTAATTTTTGGAAA
61838 ATTCAGGGAC
Statistics
Matches: 282, Mismatches: 47, Indels: 36
0.77 0.13 0.10
Matches are distributed among these distances:
27 1 0.00
28 16 0.06
29 63 0.22
30 175 0.62
31 13 0.05
32 14 0.05
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAAGTTTGAGGGTT
Found at i:61845 original size:29 final size:29
Alignment explanation
Indices: 61754--61845 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
61744 GGAAAGTTTG
* * *
61754 AGGGTTAAAACGTAATTTTTGGAAAATTT
1 AGGGTCAAAACGTAATTTTTAGAAAATTA
** *
61783 AGAGGTCAAAATATAATTTTTA-AAAGTTTA
1 AG-GGTCAAAACGTAATTTTTAGAAA-ATTA
* *
61813 AGGGTCAAAACGTGATTTTTAGAAAATTC
1 AGGGTCAAAACGTAATTTTTAGAAAATTA
61842 AGGG
1 AGGG
61846 ACCTTTTGGG
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 27 0.55
30 22 0.45
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.34
Consensus pattern (29 bp):
AGGGTCAAAACGTAATTTTTAGAAAATTA
Found at i:63599 original size:17 final size:17
Alignment explanation
Indices: 63555--63625 Score: 61
Period size: 17 Copynumber: 4.2 Consensus size: 17
63545 TTTATTTCAG
* **
63555 AATAAATTTAAACTCCA
1 AATAAATTTAAATTTAA
** *
63572 AATAAGCTTAAATTTAC
1 AATAAATTTAAATTTAA
*
63589 AATAAATTTAAACTTAA
1 AATAAATTTAAATTTAA
* *
63606 AATGAATTAAAATTTAA
1 AATAAATTTAAATTTAA
63623 AAT
1 AAT
63626 CTTAAAATGG
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (17 bp):
AATAAATTTAAATTTAA
Found at i:63619 original size:34 final size:33
Alignment explanation
Indices: 63555--63621 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
63545 TTTATTTCAG
*
63555 AATAAATTTAAACTCCAAATAAGCTTAAATTTAC
1 AATAAATTTAAACTCAAAATAA-CTTAAATTTAC
*
63589 AATAAATTTAAACTTAAAATGAA-TTAAAATTTA
1 AATAAATTTAAACTCAAAAT-AACTT-AAATTTA
63622 AAATCTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 2 0.07
34 25 0.86
35 2 0.07
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.34
Consensus pattern (33 bp):
AATAAATTTAAACTCAAAATAACTTAAATTTAC
Found at i:67924 original size:24 final size:26
Alignment explanation
Indices: 67897--67944 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
67887 AGAGAAATGT
67897 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
67921 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
67945 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:68033 original size:23 final size:22
Alignment explanation
Indices: 68007--68078 Score: 57
Period size: 23 Copynumber: 3.5 Consensus size: 22
67997 ACACTAGTGC
68007 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTG-TTAGCACTTTGTGT
*
68030 G--CTCAG-TA---CTTTGTGT
1 GCTCTCTGTTAGCACTTTGTGT
* *
68046 ACTCTTTGTTTAGCACTTTGTGT
1 GCTCTCTG-TTAGCACTTTGTGT
68069 GCTCTCTGTT
1 GCTCTCTGTT
68079 GCCCAGCACT
Statistics
Matches: 36, Mismatches: 6, Indels: 15
0.63 0.11 0.26
Matches are distributed among these distances:
16 8 0.22
18 3 0.08
19 2 0.06
20 2 0.06
21 4 0.11
22 2 0.06
23 15 0.42
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (22 bp):
GCTCTCTGTTAGCACTTTGTGT
Found at i:68258 original size:12 final size:12
Alignment explanation
Indices: 68241--68267 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
68231 TACATTGAGG
68241 TAAGTGAAATGA
1 TAAGTGAAATGA
68253 TAAGTGAAATGA
1 TAAGTGAAATGA
68265 TAA
1 TAA
68268 ATACATGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.22, T:0.26
Consensus pattern (12 bp):
TAAGTGAAATGA
Found at i:72469 original size:2 final size:2
Alignment explanation
Indices: 72462--72493 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
72452 CCTCCCATTT
72462 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
72494 AATGGATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:85305 original size:9 final size:9
Alignment explanation
Indices: 85291--85319 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
85281 TATTTTTATT
85291 TTTAAAATA
1 TTTAAAATA
85300 TTTAAAATA
1 TTTAAAATA
85309 TTTAAAATA
1 TTTAAAATA
85318 TT
1 TT
85320 AATATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTTAAAATA
Found at i:86473 original size:24 final size:24
Alignment explanation
Indices: 86446--86494 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
86436 TAAGAACAAA
86446 CCTTATGATTCTATAGGTCACTCT
1 CCTTATGATTCTATAGGTCACTCT
86470 CCTTATGATTCTATAGGTCACTCT
1 CCTTATGATTCTATAGGTCACTCT
86494 C
1 C
86495 AACACTCGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.27, G:0.12, T:0.41
Consensus pattern (24 bp):
CCTTATGATTCTATAGGTCACTCT
Found at i:87858 original size:22 final size:22
Alignment explanation
Indices: 87809--87859 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
87799 TGTAAAATAA
* *
87809 AAAGGAATAGTAATTTCAGTTT
1 AAAGTAATAGTAATTTCAGATT
87831 AAAGTAATAGTAATTTC-GATT
1 AAAGTAATAGTAATTTCAGATT
87852 AACAGTAA
1 AA-AGTAA
87860 CCTGTTTCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (22 bp):
AAAGTAATAGTAATTTCAGATT
Found at i:99857 original size:23 final size:23
Alignment explanation
Indices: 99788--99863 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 23
99778 TCGTTCATAC
99788 AATTTTATT-ATATATT-ATCTTAT
1 AATTTT-TTCATATATTAAT-TTAT
* * **
99811 AATTTTTTCATGAGA-CAAGGTAT
1 AATTTTTTCAT-ATATTAATTTAT
99834 AATTTTTTCATATATTAATTTAT
1 AATTTTTTCATATATTAATTTAT
99857 AATTTTT
1 AATTTTT
99864 ATTATTTATA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
22 4 0.10
23 34 0.83
24 3 0.07
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (23 bp):
AATTTTTTCATATATTAATTTAT
Found at i:101330 original size:16 final size:17
Alignment explanation
Indices: 101291--101331 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
101281 ATAATAAAAA
*
101291 TATAATTTTATTATTTT
1 TATAAATTTATTATTTT
*
101308 AAT-AATTTA-TATTTT
1 TATAAATTTATTATTTT
101323 TATAAATTT
1 TATAAATTT
101332 GAGATGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 8 0.40
16 10 0.50
17 2 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATAAATTTATTATTTT
Found at i:102936 original size:18 final size:18
Alignment explanation
Indices: 102913--102958 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
102903 AAACATGCGC
102913 TTCTGCAAAATACCCAAA
1 TTCTGCAAAATACCCAAA
102931 TTCTGCAAAATACCCAAA
1 TTCTGCAAAATACCCAAA
102949 TTCTGCAAAA
1 TTCTGCAAAA
102959 ATCTATGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.43, C:0.26, G:0.07, T:0.24
Consensus pattern (18 bp):
TTCTGCAAAATACCCAAA
Found at i:111836 original size:18 final size:18
Alignment explanation
Indices: 111798--111836 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
111788 TTTTTTGTAA
**
111798 TTGTGTTGTGTTTCGTTG
1 TTGTGTTGTGTTTCGCAG
*
111816 TTGTTTTGTGTTTCGCAG
1 TTGTGTTGTGTTTCGCAG
111834 TTG
1 TTG
111837 GATGGAATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.03, C:0.08, G:0.31, T:0.59
Consensus pattern (18 bp):
TTGTGTTGTGTTTCGCAG
Found at i:114074 original size:19 final size:20
Alignment explanation
Indices: 114043--114094 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
114033 TAATTTTAAT
114043 TTTTTTACA-TTAAGAT-TTA
1 TTTTTTA-ATTTAAGATGTTA
*
114062 TTTTTTAATTTAATATGTTA
1 TTTTTTAATTTAAGATGTTA
*
114082 TTTATTTATTTTA
1 TTT-TTTAATTTA
114095 TTATTTTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 1 0.04
19 13 0.46
20 6 0.21
21 8 0.29
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (20 bp):
TTTTTTAATTTAAGATGTTA
Found at i:114607 original size:18 final size:20
Alignment explanation
Indices: 114574--114614 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
114564 CTACACATTG
*
114574 TGTAATTTTATATTTTTTTT
1 TGTAATTTTATATTTTTCTT
114594 TGTAA-TTT-TATTTTTCTT
1 TGTAATTTTATATTTTTCTT
114612 TGT
1 TGT
114615 GATCTTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 12 0.60
19 3 0.15
20 5 0.25
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.73
Consensus pattern (20 bp):
TGTAATTTTATATTTTTCTT
Found at i:124345 original size:22 final size:22
Alignment explanation
Indices: 124315--124356 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
124305 AAATAAGTTT
**
124315 TTGTATTTTTTTGAAAAAATAA
1 TTGTATTTTAATGAAAAAATAA
*
124337 TTGTTTTTTAATGAAAAAAT
1 TTGTATTTTAATGAAAAAAT
124357 GTATTTAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (22 bp):
TTGTATTTTAATGAAAAAATAA
Found at i:125772 original size:29 final size:29
Alignment explanation
Indices: 125695--126062 Score: 266
Period size: 29 Copynumber: 12.6 Consensus size: 29
125685 TTCGAGATCG
* * *
125695 AAAATGGAGTTTTTGGACA--TCCGGGGGT
1 AAAATGGAATTTTTGGA-AGTTTCGGGGTT
** *
125723 AAAATGGTAATTTTTTAAAGTTTCGGAGTT
1 AAAATGG-AATTTTTGGAAGTTTCGGGGTT
* *
125753 AAAAT-GAGATTTTTGGAAGTTTTGAGGTT
1 AAAATGGA-ATTTTTGGAAGTTTCGGGGTT
* *
125782 AAAAATGGAATTTTTGGAAGTTTAGGGGTA
1 -AAAATGGAATTTTTGGAAGTTTCGGGGTT
* * *
125812 AAAATGGAATTTCTGAAAG-TTCGGGGGT
1 AAAATGGAATTTTTGGAAGTTTCGGGGTT
*
125840 AAAATTGGAATTTTT-GATAG-TTCGGGGGT
1 AAAA-TGGAATTTTTGGA-AGTTTCGGGGTT
* * *
125869 AAAATGGAATTTTTGGAAGTTTTGAGGTAAA
1 AAAATGGAATTTTTGGAAGTTTCGGGGT--T
* * *
125900 AAAATGGAACTTTTGGAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTT
** * *
125929 AAAATGGAATTTTTTAAAG-TTCGAGTGTA
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTT
* *
125958 AAAATGGAATTTTTGGATGTTTAGGGG-T
1 AAAATGGAATTTTTGGAAGTTTCGGGGTT
* * * *
125986 AAAATTGGAATTTTTAGAAGTTTTGAGGTA
1 AAAA-TGGAATTTTTGGAAGTTTCGGGGTT
* ** *
126016 AAAATTGAATTTTTGGAAGTTTCAAGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-T
*
126046 AAAATGTAATTTTTGGA
1 AAAATGGAATTTTTGGA
126063 TAGATTAGGG
Statistics
Matches: 273, Mismatches: 50, Indels: 32
0.77 0.14 0.09
Matches are distributed among these distances:
28 39 0.14
29 150 0.55
30 57 0.21
31 27 0.10
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTT
Found at i:125796 original size:58 final size:59
Alignment explanation
Indices: 125723--126037 Score: 322
Period size: 58 Copynumber: 5.4 Consensus size: 59
125713 ATCCGGGGGT
** * *
125723 AAAATGGTAATTTTTTAAAGTTTCGGAGTTAAAAT-GAGATTTTTGGAAGTTTTGAGGTTA
1 AAAATGG-AATTTTTGGAAGTTTAGGGGTTAAAATGGA-ATTTTTGGAAGTTTTGAGGTTA
* * * * * *
125783 AAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTCTGAAAG-TTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTAGGGGTTAAAATGGAATTTTTGGAAGTTTTGAGGTTA
* * * *
125841 AAATTGGAATTTTT-GATAG-TTCGGGGGTAAAATGGAATTTTTGGAAGTTTTGAGGTAAA
1 AAAATGGAATTTTTGGA-AGTTTAGGGGTTAAAATGGAATTTTTGGAAGTTTTGAGGT-TA
* * ** *
125900 AAAATGGAACTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTTAAAG-TTCGA-GTGTA
1 AAAATGGAATTTTTGGAAGTTTAGGGGTTAAAATGGAATTTTTGGAAGTTTTGAGGT-TA
* *
125958 AAAATGGAATTTTTGGATGTTTAGGGG-TAAAATTGGAATTTTTAGAAGTTTTGAGG-TA
1 AAAATGGAATTTTTGGAAGTTTAGGGGTTAAAA-TGGAATTTTTGGAAGTTTTGAGGTTA
*
126016 AAAATTGAATTTTTGGAAGTTT
1 AAAATGGAATTTTTGGAAGTTT
126038 CAAGGTCAAA
Statistics
Matches: 208, Mismatches: 38, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
57 29 0.14
58 90 0.43
59 54 0.26
60 35 0.17
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.37
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTTAGGGGTTAAAATGGAATTTTTGGAAGTTTTGAGGTTA
Found at i:125914 original size:117 final size:114
Alignment explanation
Indices: 125716--126037 Score: 423
Period size: 117 Copynumber: 2.8 Consensus size: 114
125706 TTTGGACATC
* * * *
125716 CGGGGGTAAAATGGTAATTTTTTAAAGTTTCGGAGTTAAAAT-GAGATTTTTGGAAGTTTTGAGG
1 CGGGGGTAAAATGG-AATTTTTGATAG-TTCGGGGGTAAAATGGA-ATTTTTGGAAGTTTTGAGG
125780 TTAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTCTGAAAGTT
63 -TAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTCTGAAAGTT
125833 CGGGGGTAAAATTGGAATTTTTGATAGTTCGGGGGTAAAATGGAATTTTTGGAAGTTTTGAGGTA
1 CGGGGGTAAAA-TGGAATTTTTGATAGTTCGGGGGTAAAATGGAATTTTTGGAAGTTTTGAGGT-
* * *
125898 AAAAAATGGAACTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTTAAAGTT
64 -AAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTCTGAAAGTT
* * ** *
125950 CGAGTGTAAAAATGGAATTTTTGGAT-GTTTAGGGGTAAAATTGGAATTTTTAGAAGTTTTGAGG
1 CGGGGGT-AAAATGGAATTTTT-GATAGTTCGGGGGTAAAA-TGGAATTTTTGGAAGTTTTGAGG
*
126014 TAAAAATTGAATTTTTGGAAGTTT
63 TAAAAATGGAATTTTTGGAAGTTT
126038 CAAGGTCAAA
Statistics
Matches: 184, Mismatches: 14, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
115 1 0.01
116 52 0.28
117 98 0.53
118 33 0.18
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (114 bp):
CGGGGGTAAAATGGAATTTTTGATAGTTCGGGGGTAAAATGGAATTTTTGGAAGTTTTGAGGTAA
AAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTCTGAAAGTT
Found at i:127833 original size:23 final size:23
Alignment explanation
Indices: 127801--127848 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
127791 ACTAGACATT
127801 ATTTAAATAAATTTAAATTT-AA
1 ATTTAAATAAATTTAAATTTCAA
127823 ATTTATAATAAATTTAAATTTCAA
1 ATTTA-AATAAATTTAAATTTCAA
127847 AT
1 AT
127849 AAATTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 5 0.21
23 15 0.62
24 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAAATAAATTTAAATTTCAA
Found at i:127836 original size:17 final size:17
Alignment explanation
Indices: 127814--127893 Score: 115
Period size: 17 Copynumber: 4.7 Consensus size: 17
127804 TAAATAAATT
*
127814 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
*
127831 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
127848 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
** *
127865 TAACCTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
127882 TAAATTTAAATT
1 TAAATTTAAATT
127894 CTATTAGGCC
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 54 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:127851 original size:11 final size:10
Alignment explanation
Indices: 127801--127858 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
127791 ACTAGACATT
127801 ATTTAAATAA
1 ATTTAAATAA
127811 ATTTAAATTTAA
1 ATTTAAA--TAA
127823 ATTTATAATAA
1 ATTTA-AATAA
127834 ATTTAAAT--
1 ATTTAAATAA
*
127842 -TTCAAATAA
1 ATTTAAATAA
127851 ATTTAAAT
1 ATTTAAAT
127859 TTAAAATAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 6 0.15
10 16 0.40
11 8 0.20
12 8 0.20
13 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (10 bp):
ATTTAAATAA
Found at i:127857 original size:23 final size:23
Alignment explanation
Indices: 127806--127863 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
127796 ACATTATTTA
**
127806 AATAAATTTAAATTTAAATTTAT
1 AATAAATTTAAATTTAAATAAAT
127829 AATAAATTTAAATTTCAAATAAAT
1 AATAAATTTAAATTT-AAATAAAT
*
127853 -TTAAATTTAAA
1 AATAAATTTAAA
127864 ATAACCTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 25 0.81
24 6 0.19
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
AATAAATTTAAATTTAAATAAAT
Found at i:127865 original size:7 final size:6
Alignment explanation
Indices: 127808--127893 Score: 67
Period size: 6 Copynumber: 15.0 Consensus size: 6
127798 ATTATTTAAA
127808 TAAATT TAAATT TAAATT TATAA-- TAAATT TAAATT TCAAA-- TAAATT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT
* ** * *
127854 TAAATT TAAA-A TAACCT TAATTT TAAA-A TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
127894 CTATTAGGCC
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
4 5 0.08
5 10 0.16
6 44 0.69
7 5 0.08
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:131919 original size:18 final size:18
Alignment explanation
Indices: 131898--131935 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
131888 TGAATTTTCG
131898 AATTCAAAT-AACTCGAAT
1 AATTCAAATAAAC-CGAAT
*
131916 AATTCGAATAAACCGAAT
1 AATTCAAATAAACCGAAT
131934 AA
1 AA
131936 AACTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.53, C:0.16, G:0.08, T:0.24
Consensus pattern (18 bp):
AATTCAAATAAACCGAAT
Found at i:133926 original size:18 final size:17
Alignment explanation
Indices: 133886--133927 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
133876 AATATTTACA
133886 TCTTGTGTATTTTGATTT
1 TCTT-TGTATTTTGATTT
*
133904 T-TTTGTAGTTTTGTTTT
1 TCTTTGTA-TTTTGATTT
133921 TCTTTGT
1 TCTTTGT
133928 GACCATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.19
17 11 0.52
18 6 0.29
ACGTcount: A:0.07, C:0.05, G:0.17, T:0.71
Consensus pattern (17 bp):
TCTTTGTATTTTGATTT
Found at i:135059 original size:16 final size:17
Alignment explanation
Indices: 135031--135070 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
135021 AGTATAGCGT
135031 AAATTTT-TAATTTA-A
1 AAATTTTATAATTTATA
*
135046 ATATTTTATAATTTATA
1 AAATTTTATAATTTATA
135063 AAATTTTA
1 AAATTTTA
135071 AGATAGTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 6 0.29
16 7 0.33
17 8 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AAATTTTATAATTTATA
Found at i:135127 original size:31 final size:30
Alignment explanation
Indices: 135084--135146 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
135074 TAGTAATGAT
135084 AAAATTATATTTTGAT-TCTTTAAAAATAATA
1 AAAATTATATTTT-ATCT-TTTAAAAATAATA
*
135115 AAAATT-TAATTTTATCTTTTAAAAATTATA
1 AAAATTAT-ATTTTATCTTTTAAAAATAATA
135145 AA
1 AA
135147 TATATAGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 17 0.59
31 12 0.41
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (30 bp):
AAAATTATATTTTATCTTTTAAAAATAATA
Found at i:146701 original size:29 final size:29
Alignment explanation
Indices: 146668--146725 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
146658 TTTTAGATAG
146668 TTGCAGCTTGTAAGATGCATTTGCAGACT
1 TTGCAGCTTGTAAGATGCATTTGCAGACT
146697 TTGCAGCTTGTAAGATGCATTTGCAGACT
1 TTGCAGCTTGTAAGATGCATTTGCAGACT
146726 GCAAGGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (29 bp):
TTGCAGCTTGTAAGATGCATTTGCAGACT
Found at i:150772 original size:11 final size:11
Alignment explanation
Indices: 150756--150809 Score: 108
Period size: 11 Copynumber: 4.9 Consensus size: 11
150746 TCTTTAAACC
150756 TTTTTGCTCTA
1 TTTTTGCTCTA
150767 TTTTTGCTCTA
1 TTTTTGCTCTA
150778 TTTTTGCTCTA
1 TTTTTGCTCTA
150789 TTTTTGCTCTA
1 TTTTTGCTCTA
150800 TTTTTGCTCT
1 TTTTTGCTCT
150810 TAACTTGCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 43 1.00
ACGTcount: A:0.07, C:0.19, G:0.09, T:0.65
Consensus pattern (11 bp):
TTTTTGCTCTA
Found at i:150817 original size:22 final size:22
Alignment explanation
Indices: 150756--150817 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
150746 TCTTTAAACC
**
150756 TTTTTGCTCTATTTTTGCTCTA
1 TTTTTGCTCTATACTTGCTCTA
**
150778 TTTTTGCTCTATTTTTGCTCTA
1 TTTTTGCTCTATACTTGCTCTA
150800 TTTTTGCTCT-TAACTTGC
1 TTTTTGCTCTAT-ACTTGC
150818 AACCGGATGG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 1 0.03
22 36 0.97
ACGTcount: A:0.10, C:0.19, G:0.10, T:0.61
Consensus pattern (22 bp):
TTTTTGCTCTATACTTGCTCTA
Found at i:151163 original size:16 final size:15
Alignment explanation
Indices: 151138--151173 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
151128 TTCAACTCGA
151138 TTAATTTTTAAATTT
1 TTAATTTTTAAATTT
151153 TTAAGTTTTTAAATTT
1 TTAA-TTTTTAAATTT
*
151169 ATAAT
1 TTAAT
151174 ATTATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (15 bp):
TTAATTTTTAAATTT
Found at i:153322 original size:18 final size:16
Alignment explanation
Indices: 153290--153330 Score: 59
Period size: 14 Copynumber: 2.7 Consensus size: 16
153280 ATGAAATGAG
153290 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
153306 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
153320 ATTAAATTTTT
1 AATAAATTTTT
153331 TAAACCCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 13 0.59
16 9 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:154834 original size:6 final size:6
Alignment explanation
Indices: 154823--154850 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
154813 TGCATGTCGG
154823 TGATGC TGATGC TGATGC TGATGC TGAT
1 TGATGC TGATGC TGATGC TGATGC TGAT
154851 TGATTATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.32, T:0.36
Consensus pattern (6 bp):
TGATGC
Found at i:159401 original size:12 final size:12
Alignment explanation
Indices: 159384--159439 Score: 51
Period size: 12 Copynumber: 4.5 Consensus size: 12
159374 AACAAAAAAC
159384 TTAAATATTAAA
1 TTAAATATTAAA
159396 TTAAATATTGAAA
1 TTAAATATT-AAA
* *
159409 TCAAACT-TAAATA
1 TTAAA-TATTAA-A
*
159422 TTAAATATTATA
1 TTAAATATTAAA
159434 TTAAAT
1 TTAAAT
159440 CAGAAAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
12 19 0.54
13 15 0.43
14 1 0.03
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (12 bp):
TTAAATATTAAA
Found at i:159435 original size:31 final size:30
Alignment explanation
Indices: 159380--159441 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 30
159370 GAACAACAAA
159380 AAACTTAAATATTAAATTAAATATTGAAATC
1 AAACTTAAATATTAAATTAAATATT-AAATC
*
159411 AAACTTAAATATTAAA-TATTATATTAAATC
1 AAACTTAAATATTAAATTA-AATATTAAATC
159441 A
1 A
159442 GAAAAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 8 0.28
31 21 0.72
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (30 bp):
AAACTTAAATATTAAATTAAATATTAAATC
Found at i:161685 original size:28 final size:27
Alignment explanation
Indices: 161654--161707 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
161644 TTAACTACAA
*
161654 TTGTATATATTTTTATTTTTTTATTTTT
1 TTGTAAATATTTTTA-TTTTTTATTTTT
*
161682 TTGTAAATTTTTTTATTTTTTATTTT
1 TTGTAAATATTTTTATTTTTTATTTT
161708 ATTACCTAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.78
Consensus pattern (27 bp):
TTGTAAATATTTTTATTTTTTATTTTT
Done.